View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by MPG.PuRe Technological Innovation and Resources Author’s Choice © 2012 by The American Society for Biochemistry and Molecular Biology, Inc. This paper is available on line at http://www.mcponline.org Ultra High Resolution Linear Ion Trap Orbitrap Mass Spectrometer (Orbitrap Elite) Facilitates Top Down LC MS/MS and Versatile Peptide Fragmentation Modes*□S Annette Michalski‡**, Eugen Damoc§**, Oliver Lange§, Eduard Denisov§, Dirk Nolting§, Mathias Mu¨ ller§, Rosa Viner¶, Jae Schwartz¶, Philip Remes¶, Michael Belford¶, Jean-Jacques Dunyach¶, Juergen Cox‡, Stevan Horning§, Matthias Mann‡ʈ, and Alexander Makarov§ Although only a few years old, the combination of a linear In many mass spectrometric applications, the resolving ion trap with an Orbitrap analyzer has become one of the power of the instrument is of pivotal importance. Ultimate standard mass spectrometers to characterize proteins resolution has so far been obtained by Fourier Transform and proteomes. Here we describe a novel version of this Mass Spectrometry (1) and in a recent example, Marshall and instrument family, the Orbitrap Elite, which is improved in co-workers detected more than 26,000 components in a sin- three main areas. The ion transfer optics has an ion path gle spectrum of a crude oil mixture (2). In ion cyclotron reso- that blocks the line of sight to achieve more robust oper- nance (ICR)1 Fourier transform mass spectrometry, resolution ation. The tandem MS acquisition speed of the dual cell is determined by the length of the transient and by the linear ion trap now exceeds 12 Hz. Most importantly, the resolving power of the Orbitrap analyzer has been in- strength of the magnetic field. Increasingly larger magnets creased twofold for the same transient length by employ- have allowed resolution in excess of one million for small TM ing a compact, high-field Orbitrap analyzer that almost molecules. The relatively recently introduced Orbitrap ana- doubles the observed frequencies. An enhanced Fourier lyzer utilizes a different physical principle to obtain high res- Transform algorithm—incorporating phase information— olution (3–6). The signal is recorded from the image current further doubles the resolving power to 240,000 at m/z 400 produced by ion packets which oscillate around and along the for a 768 ms transient. For top-down experiments, we spindle-shaped inner electrode of the trap: the higher the combine a survey scan with a selected ion monitoring electric field, the larger the number of oscillations per unit time scan of the charge state of the protein to be fragmented and the higher the resolving power. To increase field strength, and with several HCD microscans. Despite the 120,000 several design options can be pursued, including increasing resolving power for SIM and HCD scans, the total cycle the radius of the inner electrode of the device (7). Here we time is within several seconds and therefore suitable for liquid chromatography tandem MS. For bottom-up pro- describe an Orbitrap analyzer that achieves higher resolving teomics, we combined survey scans at 240,000 resolving power through reduced trap dimensions. Resolution is further power with data-dependent collision-induced dissocia- increased by making use of the phase information during tion of the 20 most abundant precursors in a total cycle Fourier Transformation (8–11). This ultra high resolution Or- time of 2.5 s—increasing protein identifications in com- bitrap analyzer was combined with other instrumental im- plex mixtures by about 30%. The speed of the Orbitrap provements to construct a novel linear ion trap Orbitrap hybrid Elite furthermore allows scan modes in which comple- mass spectrometer termed the Orbitrap Elite. mentary dissociation mechanisms are routinely obtained We describe principles of this instrument and characterize of all fragmented peptides. Molecular & Cellular Pro- its operation for both intact protein analysis and for bottom up teomics 11: 10.1074/mcp.O111.013698, 1–11, 2012. peptide mixture analysis. Top down protein analysis has pre- viously mainly been performed with Fourier transform (FT) ICR From the ‡Department of Proteomics and Signal Transduction, instruments because of their very high resolving power (12– Max-Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany; §Thermo Fisher Scientific (Bremen) GmbH, Hanna-Kunath-Strasse 11, 28199 Bremen, Germany; ¶Thermo Fisher 1 The abbreviations used are: AGC, automatic gain control; CID, Scientific, 355 River Oaks Parkway, San Jose, California 95134 collision induced dissociation; ETD, electron transfer dissociation; Received August 19, 2011, and in revised form, December 1, 2011 FDR, false discovery rate; FT, Fourier transform; HCD, higher energy Author’s Choice—Final version full access. collisional dissociation; HPLC, high performance liquid chromatogra- Published, MCP Papers in Press, December 12, 2011, DOI phy; ICR, ion cyclotron resonance; IPI, International Protein Index; 10.1074/mcp.O111.013698 MS/MS, tandem mass spectrometry; SIM, selected ion monitoring. Molecular & Cellular Proteomics 11.3 10.1074/mcp.O111.013698–1 Ultrahigh Resolution Linear Ion Trap Orbitrap Instrument 14). One of the challenges in using top down approaches in The combination of the 45° rotated quadrupole ion guide and the proteomics has been to obtain cycle times commensurate neutral beam blocker reduces the rate of contamination and improves the longevity of the ion optics system. A short octopole, Q00 (r 5.56 with liquid chromatography tandem MS (LC MS/MS) time 0 mm, rod diameter 2 mm, length 28.58 mm operated at 3 MHz, 800 scales (15). The linear ion trap Orbitrap has also been em- Vpp), located between the exit lens and curved quadrupole, has also ployed for top down proteomics (16–19). Here we take ad- been added and replaces the quadrupole device in this region in the vantage of the ultra high resolution of the Orbitrap Elite to LTQ Velos. This octopole tends to be more robust to contamination enable fast LC MS/MS compatible top-down scan methods. and it is also used as a dissociation device in the stand-alone Velos In bottom-up proteomics typically very complex peptide PRO (32). Faster Scan Speed—The dual cell differential pressure linear ion mixtures are analyzed (20–22). Online LC MS runs contain trap allows for substantially accelerated scan rates and higher reso- evidence for tens of thousands of peptides (23, 24) and this lution owing to the lower pressure in the mass analyzing cell of the ion places a premium on the resolution of the survey (MS) scans. trap (30). The normal scan rate on the LTQ Velos is 33,000 amu/s, A popular shotgun proteomics method on the linear ion trap which typically achieves peak widths of 0.34 amu at m/z 1822 and is Orbitrap (LTQ Orbitrap or LTQ Orbitrap Velos) is a “1 s” survey sufficient to separate isotopes of triply charged ions. By optimizing operating conditions such as the resonance ejection amplitude and scan with 60,000 resolution at m/z 400 (768 ms transient), and the phase relationship between the resonance ejection and trapping ion trap collision-induced dissociation (CID) scans of the ten RF signals, a small sacrifice in resolution can give a large improve- or twenty most abundant ions (“high resolution” “low resolu- ment in scan rate. In the Velos PRO, the scan rate has been doubled tion” or “high–low” top10 method). Here we explore topN to 66,000 amu/s while still maintaining better than unit resolution, methods with much higher resolution survey scans as well as achieving an average peak width at half height of 0.47 amu at m/z an increased number of fragmentation events per cycle en- 1822. With this rapid scan rate up to 12.5 MS/MS scans can be performed per second (rapid CID or rCID). abled by “rapid CID” scans. A “high–high” strategy (high Higher Dynamic Range Detection System—Because of the faster resolution MS as well as MS/MS (25)) has been routinely made scan rates the ion currents generated when performing mass analysis possible on Orbitrap instruments by higher energy collisional are also increased. Therefore, a higher dynamic range detection dissociation (HCD) with the advent of the LTQ-Orbitrap Velos system is required. Discrete dynode electron multipliers have been (26). We show that this strategy benefits from the shorter developed (SGE Analytical Science Pty Ltd, Australia) that replace the continuous channel electron multipliers in the LTQ Velos. These new transients and higher resolving power possible on the Or- electron multipliers have linear outputs up to 160 ␮A yielding six bitrap Elite. orders of magnitude dynamic range. A 24 bit analog-to-digital con- It has been demonstrated that a combination of two frag- verter is employed in the electrometer circuitry which matches the mentation methods can greatly augment sequence related performance of the discrete dynode multipliers. The wider linear information in peptide MS/MS (27–29) and we explore this dynamic range of this detection system increases the precision and dual approach with CID and HCD fragmentation of the same accuracy for doing quantitative analysis while also offering enhanced limits of detection. precursor ions. High-field Orbitrap Analyzer—The Orbitrap mass analyzer generally consists of an outer barrel-like electrode of maximum radius R2 and EXPERIMENTAL PROCEDURES a central spindle-like electrode along the axis of maximum radius R1, The Orbitrap Elite is a further development of the LTQ Orbitrap with the outer electrode maintained at the virtual ground of the pre- Ͼ Velos (26). This hybrid instrument combines a Velos PRO dual cell amplifier, while the central electrode is at a voltage -Ur (Ur 0 for ϭ differential pressure linear ion trap mass spectrometer with a high positive ions) (3).